The scipion-chem-fpocket from scipion-chem

scipion-chem-fpocket's Introduction

Fpocket plugin

Documentation under development, sorry for the inconvenience

This is a Scipion plugin that offers different tools from the FPocket suite. These tools will make it possible to carry out different functions for predicting protein pockets.

You can find further information on the plugin documentation.

Install this plugin

You will need to first install Scipion3 and Scipion-chem to run these protocols.

Install the plugin in Scipion

Fpocket is installed automatically by scipion.

Install the stable version (Not available yet)

Through the plugin manager GUI by launching Scipion and following Configuration >> Plugins

or

scipion3 installp -p scipion-chem-fpocket

Developer's version
1. Download repository:
```
git clone https://github.com/scipion-chem/scipion-chem-fpocket.git
```
1. Switch to the desired branch (master or devel):
Scipion-chem-fpocket is constantly under development and including new features. If you want a relatively older an more stable version, use master branch (default). If you want the latest changes and developments, user devel branch.
```
cd scipion-chem-fpocket
git checkout devel
```
1. Install:
```
scipion3 installp -p path_to_scipion-chem-fpocket --devel
```

scipion-chem-fpocket's People

Contributors

scipion-chem-fpocket's Issues

Find pockets unexpected crush

00001:   Logging configured. STDOUT --> Runs/000155_FpocketFindPockets/logs/run.stdout , STDERR --> Runs/000155_FpocketFindPockets/logs/run.stderr
00002:   RUNNING PROTOCOL -----------------
00003:   Protocol starts
00004:   Hostname: ruben-GL502VSK
00005:   PID: 14459
00006:   pyworkflow: 3.0.17
00007:   plugin: fpocket
00008:   currentDir: /home/ruben/ScipionUserData/projects/chemoinfo
00009:   workingDir: Runs/000155_FpocketFindPockets
00010:   runMode: Restart
00011:             MPI: 1
00012:         threads: 1
00013:    Starting at step: 1
00014:    Running steps 
00015:   STARTED: convertInputStep, step 1, time 2021-10-26 11:56:03.861915
00016:   FINISHED: convertInputStep, step 1, time 2021-10-26 11:56:03.932502
00017:   STARTED: fPocketStep, step 2, time 2021-10-26 11:56:04.032080
00018:   fpocket - Find pockets
00019:    /home/ruben/app/scipion3/software/em/fpocket-3.0/bin/fpocket "-f" "/home/ruben/ScipionUserData/projects/chemoinfo/Runs/000155_FpocketFindPockets/extra/nsp13-x0020_0B_apo-desolv.pdb" "-m" "3.4" "-M" "6.2" "-i" "15" "-p" "0.0" "-A" "3" "-C" "s" "-e" "e" "-D" "2.4" "-v" "300"
00020:   ***** POCKET HUNTING BEGINS ***** 
00021:   ***** POCKET HUNTING ENDS ***** 
00022:   FINISHED: fPocketStep, step 2, time 2021-10-26 11:56:05.608947
00023:   STARTED: createOutputStep, step 3, time 2021-10-26 11:56:05.733832
00024:   Protocol failed: expected str, bytes or os.PathLike object, not NoneType
00025:   FAILED: createOutputStep, step 3, time 2021-10-26 11:56:06.135884
00026:   *** Last status is failed 
00027:   ------------------- PROTOCOL FAILED (DONE 3/3)
``
[nsp13-x0020_0B_apo-desolv.pdb.zip](https://github.com/scipion-chem/scipion-chem-fpocket/files/7418071/nsp13-x0020_0B_apo-desolv.pdb.zip)
`

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